FindAdapter: Use AdapterRemoval to identify adapters

In esATAC: An Easy-to-use Systematic pipeline for ATACseq data analysis

Description

Use AdapterRemoval to identify adapters for paired end data

Usage

atacFindAdapter(
  atacProc,
  fastqInput1 = NULL,
  fastqInput2 = NULL,
  reportPrefix = NULL,
  interleave = FALSE,
  findParamList = NULL,
  threads = getThreads(),
  ...
)

## S4 method for signature 'ATACProc'
atacFindAdapter(
  atacProc,
  fastqInput1 = NULL,
  fastqInput2 = NULL,
  reportPrefix = NULL,
  interleave = FALSE,
  findParamList = NULL,
  threads = getThreads(),
  ...
)

findAdapter(
  fastqInput1,
  fastqInput2 = NULL,
  reportPrefix = NULL,
  interleave = FALSE,
  findParamList = NULL,
  threads = getThreads(),
  ...
)

Arguments

atacProc	ATACProc-class object scalar. It has to be the return value of upstream process: atacRenamer renamer atacUnzipAndMerge unzipAndMerge
fastqInput1	Character vector. For single-end sequencing, it contains sequence file paths. For paired-end sequencing, it can be file paths with #1 mates paired with file paths in fastqInput2 And it can also be interleaved file paths when argument interleaved=TRUE
fastqInput2	Character vector. It contains file paths with #2 mates paired with file paths in fastqInput1 For single-end sequencing files and interleaved paired-end sequencing files(argument interleaved=TRUE), it must be NULL.
reportPrefix	Character. The prefix of report files path. Default: generate from known parameters
interleave	Logical. Set TRUE when files are interleaved paired-end sequencing data.
findParamList	Additional arguments to be passed on to the binaries for identifying adapter. See below for details.
threads	The number of threads used in this step.
...	Additional arguments, currently unused.

Details

The parameter related to input and output file path will be automatically obtained from ATACProc-class object or generated based on known parameters if their values are default(e.g. NULL). Otherwise, the generated values will be overwrited. If you want to use this function independently, you can use findAdapter instead. You can put all aditional arguments in one Character(e.g. "–threads 8") with white space splited just like command line, or put them in Character vector(e.g. c("–threads","8")). Note that some arguments( "–file1","–file2","–adapter1","–adapter2","–output1","–output2", "–basename","–interleaved","thread") to the findParamList are invalid if they are already handled as explicit function arguments. See the output of adapterremoval_usage() for details about available parameters.

Value

An invisible ATACProc-class object scalar for downstream analysis.

Author(s)

Zheng Wei

See Also

atacRenamer renamer atacUnzipAndMerge unzipAndMerge atacBowtie2Mapping

Examples

library(magrittr)
td <- tempdir()
setTmpDir(td)

# Identify adapters
prefix<-system.file(package="esATAC", "extdata", "uzmg")
(reads_1 <-file.path(prefix,"m1",dir(file.path(prefix,"m1"))))
(reads_2 <-file.path(prefix,"m2",dir(file.path(prefix,"m2"))))

reads_merged_1 <- file.path(td,"reads1.fastq")
reads_merged_2 <- file.path(td,"reads2.fastq")
atacproc <-
atacUnzipAndMerge(fastqInput1 = reads_1,fastqInput2 = reads_2) %>%
atacRenamer %>% atacFindAdapter

dir(td)

esATAC documentation built on Nov. 8, 2020, 6:58 p.m.